A high performance framework for modeling and simulation of large-scale complex systems

2015 ◽  
Vol 51 ◽  
pp. 132-141 ◽  
Author(s):  
Feng Zhu ◽  
Yiping Yao ◽  
Wenjie Tang ◽  
Dan Chen
Keyword(s):  
Complex Systems ◽  
Modeling And Simulation ◽  
High Performance ◽  
Large Scale ◽  
Performance Framework

Scaling modeling and simulation on high-performance computing clusters

SIMULATION ◽  
2019 ◽  
Vol 96 (2) ◽  
pp. 221-232
Author(s):  
Mike Mikailov ◽  
Junshan Qiu ◽  
Fu-Jyh Luo ◽  
Stephen Whitney ◽  
Nicholas Petrick
Keyword(s):  
Modeling And Simulation ◽  
High Performance Computing ◽  
Message Passing ◽  
High Performance ◽  
Large Scale ◽  
Message Passing Interface ◽  
The United States ◽  
United States Food ◽  
States Food ◽  
Performance Computing

Large-scale modeling and simulation (M&S) applications that do not require run-time inter-process communications can exhibit scaling problems when migrated to high-performance computing (HPC) clusters if traditional software parallelization techniques, such as POSIX multi-threading and the message passing interface, are used. A comprehensive approach for scaling M&S applications on HPC clusters has been developed and is called “computation segmentation.” The computation segmentation is based on the built-in array job facility of job schedulers. If used correctly for appropriate applications, the array job approach provides significant benefits that are not obtainable using other methods. The parallelization illustrated in this paper becomes quite complex in its own right when applied to extremely large M&S tasks, particularly due to the need for nested loops. At the United States Food and Drug Administration, the approach has provided unsurpassed efficiency, flexibility, and scalability for work that can be performed using embarrassingly parallel algorithms.

scholarly journals Pyntacle: a parallel computing-enabled framework for large-scale network biology analysis

GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Luca Parca ◽  
Mauro Truglio ◽  
Tommaso Biagini ◽  
Stefano Castellana ◽  
Francesco Petrizzelli ◽  
...  
Keyword(s):  
Parallel Computing ◽  
High Performance ◽  
Large Scale ◽  
Critical Groups ◽  
Natural Systems ◽  
Performance Framework ◽  
Large Scale Network ◽  
Potential Applications ◽  
Scale Network ◽  
Computational Resources

Abstract Background Some natural systems are big in size, complex, and often characterized by convoluted mechanisms of interaction, such as epistasis, pleiotropy, and trophism, which cannot be immediately ascribed to individual natural events or biological entities but that are often derived from group effects. However, the determination of important groups of entities, such as genes or proteins, in complex systems is considered a computationally hard task. Results We present Pyntacle, a high-performance framework designed to exploit parallel computing and graph theory to efficiently identify critical groups in big networks and in scenarios that cannot be tackled with traditional network analysis approaches. Conclusions We showcase potential applications of Pyntacle with transcriptomics and structural biology data, thereby highlighting the outstanding improvement in terms of computational resources over existing tools.

scholarly journals Cells in Silico – introducing a high-performance framework for large-scale tissue modeling

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Marco Berghoff ◽  
Jakob Rosenbauer ◽  
Felix Hoffmann ◽  
Alexander Schug
Keyword(s):  
In Silico ◽  
High Performance ◽  
Large Scale ◽  
Computational Models ◽  
Modular Design ◽  
Model Simulation ◽  
Three Dimensional ◽  
Cellular Potts Model ◽  
Performance Framework ◽  
Wide Range

Abstract Background Discoveries in cellular dynamics and tissue development constantly reshape our understanding of fundamental biological processes such as embryogenesis, wound-healing, and tumorigenesis. High-quality microscopy data and ever-improving understanding of single-cell effects rapidly accelerate new discoveries. Still, many computational models either describe few cells highly detailed or larger cell ensembles and tissues more coarsely. Here, we connect these two scales in a joint theoretical model. Results We developed a highly parallel version of the cellular Potts model that can be flexibly applied and provides an agent-based model driving cellular events. The model can be modular extended to a multi-model simulation on both scales. Based on the NAStJA framework, a scaling implementation running efficiently on high-performance computing systems was realized. We demonstrate independence of bias in our approach as well as excellent scaling behavior. Conclusions Our model scales approximately linear beyond 10,000 cores and thus enables the simulation of large-scale three-dimensional tissues only confined by available computational resources. The strict modular design allows arbitrary models to be configured flexibly and enables applications in a wide range of research questions. Cells in Silico (CiS) can be easily molded to different model assumptions and help push computational scientists to expand their simulations to a new area in tissue simulations. As an example we highlight a 10003 voxel-sized cancerous tissue simulation at sub-cellular resolution.

The Structure and Properties of MoSi2 Thin Film in Mos Process

1980 ◽  
Vol 38 ◽  
pp. 326-327
Author(s):  
C.K. Wu ◽  
P. Chang ◽  
N. Godinho
Keyword(s):  
Thin Film ◽  
Integrated Circuits ◽  
High Performance ◽  
Large Scale ◽  
Process Development ◽  
Structure And Properties ◽  
Metal Silicides ◽  
High Oxidation ◽  
Important Approach ◽  
High Oxidation Resistance

Recently, the use of refractory metal silicides as low resistivity, high temperature and high oxidation resistance gate materials in large scale integrated circuits (LSI) has become an important approach in advanced MOS process development (1). This research is a systematic study on the structure and properties of molybdenum silicide thin film and its applicability to high performance LSI fabrication.

RECOMMENDATIONS FOR THE CHOICE OF MILKING INSTALLATIONS IN LOOSE HOUSING SYSTEMS OF COWS

2020 ◽  
Author(s):  
В.В. ГОРДЕЕВ ◽  
В.Е. ХАЗАНОВ
Keyword(s):  
Dairy Cows ◽  
High Performance ◽  
Large Scale ◽  
Dairy Farms ◽  
Economic Indicators ◽  
Technical Level ◽  
Housing Systems ◽  
Working Shift ◽  
Technical And Economic Indicators

При выборе типа доильной установки и ее размера необходимо учитывать максимальное планируемое поголовье дойных коров и размер технологической группы, кратность и время одного доения, продолжительность рабочей смены дояров. Анализ технико-экономических показателей наиболее распространенных на сегодняшний день типов доильных установок одинакового технического уровня свидетельствует, что наилучшие удельные показатели имеет установка типа «Карусель» (1), а установка типа «Елочка» (2) требует более высоких затрат труда и средств. Установка «Параллель» (3) занимает промежуточное положение. Из анализа пропускной способности и количества необходимых операторов: установка 2 рекомендована для ферм с поголовьем дойного стада до 600 голов, 3 — не более 1200 дойных коров, 1 — более 1200 дойных коров. «Карусель» — наиболее рациональный, высокопроизводительный, легко автоматизируемый и, следовательно, перспективный способ доения в залах, особенно для крупных молочных ферм. The choice of the proper type and size of milking installations needs to take into account the maximum planned number of dairy cows, the size of a technological group, the number of milkings per day, and the duration of one milking and the operator's working shift. The analysis of technical and economic indicators of currently most common types of milking machines of the same technical level revealed that the Carousel installation had the best specific indicators while the Herringbone installation featured higher labour inputs and cash costs. The Parallel installation was found somewhere in between. In terms of the throughput and the required number of operators Herringbone is recommended for farms with up to 600 dairy cows, Parallel — below 1200 dairy cows, Carousel — above 1200 dairy cows. Carousel was found the most practical, high-performance, easily automated and, therefore, promising milking system for milking parlours, especially on the large-scale dairy farms.

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